Contacts of the helix formed by residues 195 - 209 (chain A) in PDB entry 3ZXR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 3.8 51.0 + - + -
140A ASP* 4.8 1.1 + - - -
157A ALA* 4.1 4.2 - - - +
158A ILE* 3.9 8.9 - - + +
159A SER* 2.9 45.1 + - - -
193A ASP* 3.2 1.8 + - - -
194A GLN* 1.3 96.0 - - + +
196A VAL* 1.3 65.5 + - - +
197A ASP 3.4 2.5 - - - -
198A LEU* 3.3 13.8 + - + -
199A ARG* 2.9 39.6 + - - +
218A HIS* 4.0 13.7 - + - -
223A GLY 4.1 1.9 - - - -
224A GLY* 3.4 23.2 + - - -
258A LYS* 4.4 18.6 - - - -
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ALA* 4.2 12.6 - - + -
193A ASP* 3.4 38.3 + - + +
194A GLN 3.7 1.8 - - - -
195A TYR* 1.3 77.1 - - - +
197A ASP* 1.3 59.3 + - - +
199A ARG* 3.4 9.8 + - - +
200A ASP* 3.0 29.5 + - - +
34F HIS* 4.0 12.6 - - + -
84F ARG* 3.4 51.8 - - + +
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TYR 3.4 0.2 - - - -
196A VAL* 1.3 76.3 - - - +
198A LEU* 1.3 66.8 + - - +
200A ASP* 3.3 10.2 + - - +
201A LYS* 3.1 33.5 + - - +
83F PHE 4.9 3.5 - - - +
84F ARG* 3.8 16.5 - - - +
85F ALA* 3.7 31.3 + - - +
86F ALA 5.2 0.2 + - - -
255F GLN* 5.5 3.8 + - - -
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.7 24.5 - - + -
195A TYR* 3.3 19.1 + - + +
196A VAL 3.3 0.6 - - - -
197A ASP* 1.3 79.8 - - - +
199A ARG* 1.3 56.4 + - - +
201A LYS* 3.0 12.8 + - + +
202A MET* 3.0 37.0 + - + +
252A THR* 4.2 13.9 - - + +
253A ALA* 4.5 2.0 - - - -
256A ASN* 3.8 37.0 - - + +
258A LYS* 3.7 33.0 - - + -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 4.3 17.3 - - + -
193A ASP* 2.6 43.9 + - - -
195A TYR* 2.9 29.2 + - - +
196A VAL* 3.9 13.6 - - - +
198A LEU* 1.3 72.7 - - - +
200A ASP* 1.3 61.0 + - - +
202A MET* 3.2 15.5 + - - +
203A LEU* 2.8 37.3 + - + +
216A GLY 4.5 2.6 + - - -
217A HIS* 3.5 24.7 - - - +
218A HIS* 3.5 24.7 - - - +
226A ALA* 3.7 25.4 - - + +
227A GLU 4.9 2.2 - - - -
228A ILE* 4.2 8.6 - - + +
34F HIS* 4.2 9.1 + - - -
36F THR* 5.5 2.8 + - - -
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A VAL 3.0 16.5 + - - +
197A ASP* 3.4 15.1 - - - +
199A ARG* 1.3 76.5 - - - +
201A LYS* 1.3 57.1 + - + +
203A LEU* 3.2 16.4 + - - +
204A THR* 2.9 33.8 + - - -
20F TYR* 3.5 15.2 + - + -
36F THR* 4.9 0.2 - - - -
84F ARG* 2.8 47.0 + - - +
86F ALA* 3.8 24.0 - - + +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP* 3.1 22.4 + - - +
198A LEU* 3.0 14.0 + - + +
200A ASP* 1.3 72.9 - - + +
202A MET* 1.3 61.5 + - - +
204A THR* 3.4 6.0 + - - -
205A ASN* 2.9 36.7 + - - +
252A THR* 4.0 12.8 - - + -
256A ASN* 3.1 34.9 + - - +
85F ALA* 6.6 0.2 - - - -
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.8 23.8 - - + -
138A ILE* 4.0 23.3 - - + -
198A LEU* 3.0 21.1 + - + +
199A ARG* 3.4 20.6 - - - +
201A LYS* 1.3 77.6 - - - +
203A LEU* 1.3 62.0 + - - +
205A ASN* 3.3 2.6 + - - +
206A LEU* 3.0 29.7 + - - +
228A ILE* 3.8 11.9 - - + -
248A ILE* 4.4 1.0 - - - +
249A ILE* 3.7 40.8 - - + +
252A THR* 3.7 20.8 - - + +
253A ALA* 4.1 18.6 - - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ARG* 2.8 22.7 + - + +
200A ASP* 3.5 17.5 - - - +
202A MET* 1.3 75.0 - - - +
204A THR* 1.3 57.8 + - - +
206A LEU* 3.3 7.7 + - - +
207A ILE* 2.9 32.7 + - + +
213A LEU* 3.8 18.4 - - + +
215A LYS* 4.3 9.2 - - - +
216A GLY* 4.4 12.3 - - - +
228A ILE* 3.7 33.4 - - + -
20F TYR* 3.4 34.8 - - + +
36F THR* 4.4 12.6 - - + +
37F ILE* 6.4 0.2 - - - -
38F PRO* 5.9 3.4 - - + -
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ASP 2.9 14.0 + - - -
201A LYS* 3.7 7.4 - - - -
203A LEU* 1.3 73.8 - - - +
205A ASN* 1.3 62.4 + - - +
207A ILE* 3.2 7.4 + - + +
208A ASN* 2.8 47.5 + - - +
19F GLU* 4.4 11.5 + - - +
20F TYR* 2.7 24.8 + - - -
86F ALA* 5.3 1.9 - - - +
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Residues in contact with ASN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO* 4.5 21.7 - - + +
83A PHE* 3.7 12.1 - - - -
201A LYS* 2.9 20.9 + - - +
202A MET 3.8 1.3 - - - +
204A THR* 1.3 79.0 - - - +
206A LEU* 1.3 59.8 + - - +
208A ASN* 3.4 10.1 + - - +
209A SER* 2.8 29.8 + - - -
248A ILE* 3.7 19.3 - - + -
252A THR* 2.8 29.4 + - - +
255A GLN* 5.7 0.2 + - - -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A MET 3.0 21.2 + - - +
203A LEU* 3.5 6.1 - - - +
205A ASN* 1.3 73.8 - - - +
207A ILE* 1.3 66.4 + - - +
209A SER 3.0 9.9 + - - -
211A PHE* 3.1 54.3 + - + +
213A LEU* 3.9 15.7 - - + -
228A ILE* 3.7 29.8 - - + -
230A TYR* 5.6 0.7 - - + -
245A TYR* 3.9 28.3 - - + +
248A ILE* 3.9 24.2 - - + -
249A ILE* 4.1 9.4 - - + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LEU 2.9 19.3 + - - +
204A THR* 3.5 8.1 - - + +
206A LEU* 1.3 73.8 - - - +
208A ASN* 1.3 67.6 + - - +
210A GLY* 2.8 23.4 + - - -
211A PHE 3.9 10.7 + - - +
213A LEU* 3.5 22.7 - - + +
19F GLU 5.7 0.9 - - - +
20F TYR* 3.8 28.9 - - + +
38F PRO* 4.4 12.8 - - + -
40F SER* 5.7 1.6 - - - +
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Residues in contact with ASN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 5.4 3.5 - - - +
82A PRO* 5.9 4.5 - - + -
204A THR* 2.8 40.7 + - - +
205A ASN* 3.9 10.2 + - - +
207A ILE* 1.3 80.2 - - - +
209A SER* 1.3 58.0 + - - +
210A GLY 3.3 1.6 + - - -
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 3.3 31.1 + - - +
80A ILE 4.5 10.0 + - - +
82A PRO* 4.0 15.1 - - - +
205A ASN 2.8 15.9 + - - -
206A LEU 3.0 7.3 + - - -
208A ASN* 1.3 76.6 - - - +
210A GLY* 1.3 61.1 + - - +
211A PHE* 3.3 12.4 + - - -
244A LEU* 4.6 6.5 - - - -
248A ILE* 3.3 24.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il